Molecular visualization Tuomas Hätinen

Overview Introduction Visualisation styles Chime Swiss PDB Viewer Online tutorial – basic features Exercises Swiss PDB Viewer Demo – basic features Exercises – Chris Wilton assisting

Context – Central Dogma Gene → mRNA → Protein primary structure → Tertiary structure → Quaternary structure → Protein function → Phenotype

Introduction Structure determines function Structural analysis provides basis for Understanding molecular function Prediction of function Experimental design to test predictions

Structure data – textual representation Structure data is stored in PDB file format in ATOM fields

Structure data – visualisation A structure file contains large amount of data Too much for the human mind to grasp

Structure data – informative views Informative views higlighting important features First image: Fold of the myoglobin molecule and it’s prosthetic group Second image: residues within 3 Å of the heme group

Visual styles - Wireframe Example: Cysteine Stick/Wireframe: shows individual bonds and corresponding angles Without hydrogen atoms With hydrogen atoms

Visual styles - Spacefill Spacefilling: Spheres represent the electron cloud around nuclei of atoms Relative sizes of atoms and groups show up clearly Merged spheres represent share electrons (covalent bond) Without hydrogen atoms With hydrogen atoms

Visual styles – Ball and stick Allows structure to be seen shows atomic position and bonds, and a portion of volume – small spheres are centred at the nuclei of atoms Without hydrogen atoms With hydrogen atoms

Visual styles – Backbone Four amino acids shown (Lys, Ala, Ile, Thr from top to bottom) Green line is a backbone trace: all side chains removed, rods connect alpha carbon positions (or phosphate atoms) Backbone does not follow any actual bonds Right image shows backbone superimposed on tetrapeptide Used e.g. for structural superimpositions

Visual styles - Ribbon Ribbon Colour schemes shown Smooth ribbon drawn through peptide units – may either be solid (‘ribbons’) or parallel wires (‘strands’) Display the fold of a protein Colour schemes shown by secondary structure by secondary structure succession N-terminus blue C-terminus red

Visual styles - Surface Shows the surface accessible to water molecules Most useful for studying the properties of the active sites Molecular surface of lysozyme Active site in a groove Charged, hydrophilic surface

Colour schemes Colour by: Calculate molecular surface secondary structure secondary structure succession B-factor (tells the quality of the model): red  least certain, blue Accessibility to solvent red: most accessible, violet: least accessible Calculate molecular surface color by: atom type (CPK), cavity or elcetrostatic potential

Visual styles – Ramachandran plot 1

Visual styles – Ramachandran plot 2 Peptide bond Resonance in the peptide bonds partial double bond nature planar structure Bond angles ω (omega) bond angle 0° angle is defined as cis position of the main chain atoms preceding and following the bond The picture is showing 180° angles φ (phi) bond angle Cα – NH bond Ψ (psi) bond angle Cα – CO bond

Ramachandran plot 3 Main chain conformation displayed Steric hindrances restrict possible bond angles Exceptions: Glycine Proline Allowed areas shown Used for checking the quality of experimentally solved structures Tool for understanding the main chain conformation

Chime demo A web browser plugin For quick viewing Instructions: Install Chime plugin from courses folder Go to tutorial http://c4.cabrillo.cc.ca.us/projects/chime_tutorial/html/index.htm Do Chime exercises

Swiss PDB Viewer demo Also called DeepView Allows analysis of several proteins at same time Extremely versatile Linked to Swiss-Model (an automated homology modelling server – covered later in this course)

DeepView – import Enter PDB id Press here to import the file from DeepView PDB server

DeepView Accesses all the other window controls

DeepView: Main control windows

DeepView: Layers information

DeepView: Main controls (toolbar view – first part) center translation tool zoom tool rotation tool: left:rotate right: translate both: zoom world / local coordinates Instructions! read PDB file

DeepView: Main controls (toolbar – second part) distance angle dihedral angles provenance display centre fit mutation torsion

DeepView: Main controls (complete view) Accesses all the other window controls center distance angle dihedral angles provenance translation tool zoom tool rotation tool: left:rotate right: translate both: zoom display centre fit mutation torsion read PDB file world / local coordinates Instructions!

DeepView: Control Panel Current protein Chain Secondary structure type Residue

Useful functions Analysis of parts of protein Active site Oligomerization surface Superimposition of structures Magic Fit

Stereo viewing View the protein in 3D More information can be analyzed at once To toggle: Display > Stereo View (Shift+T) Recommended tutorial: http://www.usm.maine.edu/~rhodes/0Help/StereoView.html

DeepView: Links DeepView homepage DeepView tutorial http://au.expasy.org/spdbv/ DeepView tutorial http://www.usm.maine.edu/~rhodes/SPVTut/ Klotho - Small molecules in PDB format: http://www.biocheminfo.org/klotho/